1// Copyright 2016 Google Inc. 2// 3// Licensed under the Apache License, Version 2.0 (the "License"); 4// you may not use this file except in compliance with the License. 5// You may obtain a copy of the License at 6// 7// http://www.apache.org/licenses/LICENSE-2.0 8// 9// Unless required by applicable law or agreed to in writing, software 10// distributed under the License is distributed on an "AS IS" BASIS, 11// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12// See the License for the specific language governing permissions and 13// limitations under the License. 14 15// Code generated by protoc-gen-go. DO NOT EDIT. 16// versions: 17// protoc-gen-go v1.26.0 18// protoc v3.12.2 19// source: google/genomics/v1/cigar.proto 20 21package genomics 22 23import ( 24 reflect "reflect" 25 sync "sync" 26 27 _ "google.golang.org/genproto/googleapis/api/annotations" 28 protoreflect "google.golang.org/protobuf/reflect/protoreflect" 29 protoimpl "google.golang.org/protobuf/runtime/protoimpl" 30) 31 32const ( 33 // Verify that this generated code is sufficiently up-to-date. 34 _ = protoimpl.EnforceVersion(20 - protoimpl.MinVersion) 35 // Verify that runtime/protoimpl is sufficiently up-to-date. 36 _ = protoimpl.EnforceVersion(protoimpl.MaxVersion - 20) 37) 38 39// Describes the different types of CIGAR alignment operations that exist. 40// Used wherever CIGAR alignments are used. 41type CigarUnit_Operation int32 42 43const ( 44 CigarUnit_OPERATION_UNSPECIFIED CigarUnit_Operation = 0 45 // An alignment match indicates that a sequence can be aligned to the 46 // reference without evidence of an INDEL. Unlike the 47 // `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators, 48 // the `ALIGNMENT_MATCH` operator does not indicate whether the 49 // reference and read sequences are an exact match. This operator is 50 // equivalent to SAM's `M`. 51 CigarUnit_ALIGNMENT_MATCH CigarUnit_Operation = 1 52 // The insert operator indicates that the read contains evidence of bases 53 // being inserted into the reference. This operator is equivalent to SAM's 54 // `I`. 55 CigarUnit_INSERT CigarUnit_Operation = 2 56 // The delete operator indicates that the read contains evidence of bases 57 // being deleted from the reference. This operator is equivalent to SAM's 58 // `D`. 59 CigarUnit_DELETE CigarUnit_Operation = 3 60 // The skip operator indicates that this read skips a long segment of the 61 // reference, but the bases have not been deleted. This operator is commonly 62 // used when working with RNA-seq data, where reads may skip long segments 63 // of the reference between exons. This operator is equivalent to SAM's 64 // `N`. 65 CigarUnit_SKIP CigarUnit_Operation = 4 66 // The soft clip operator indicates that bases at the start/end of a read 67 // have not been considered during alignment. This may occur if the majority 68 // of a read maps, except for low quality bases at the start/end of a read. 69 // This operator is equivalent to SAM's `S`. Bases that are soft 70 // clipped will still be stored in the read. 71 CigarUnit_CLIP_SOFT CigarUnit_Operation = 5 72 // The hard clip operator indicates that bases at the start/end of a read 73 // have been omitted from this alignment. This may occur if this linear 74 // alignment is part of a chimeric alignment, or if the read has been 75 // trimmed (for example, during error correction or to trim poly-A tails for 76 // RNA-seq). This operator is equivalent to SAM's `H`. 77 CigarUnit_CLIP_HARD CigarUnit_Operation = 6 78 // The pad operator indicates that there is padding in an alignment. This 79 // operator is equivalent to SAM's `P`. 80 CigarUnit_PAD CigarUnit_Operation = 7 81 // This operator indicates that this portion of the aligned sequence exactly 82 // matches the reference. This operator is equivalent to SAM's `=`. 83 CigarUnit_SEQUENCE_MATCH CigarUnit_Operation = 8 84 // This operator indicates that this portion of the aligned sequence is an 85 // alignment match to the reference, but a sequence mismatch. This can 86 // indicate a SNP or a read error. This operator is equivalent to SAM's 87 // `X`. 88 CigarUnit_SEQUENCE_MISMATCH CigarUnit_Operation = 9 89) 90 91// Enum value maps for CigarUnit_Operation. 92var ( 93 CigarUnit_Operation_name = map[int32]string{ 94 0: "OPERATION_UNSPECIFIED", 95 1: "ALIGNMENT_MATCH", 96 2: "INSERT", 97 3: "DELETE", 98 4: "SKIP", 99 5: "CLIP_SOFT", 100 6: "CLIP_HARD", 101 7: "PAD", 102 8: "SEQUENCE_MATCH", 103 9: "SEQUENCE_MISMATCH", 104 } 105 CigarUnit_Operation_value = map[string]int32{ 106 "OPERATION_UNSPECIFIED": 0, 107 "ALIGNMENT_MATCH": 1, 108 "INSERT": 2, 109 "DELETE": 3, 110 "SKIP": 4, 111 "CLIP_SOFT": 5, 112 "CLIP_HARD": 6, 113 "PAD": 7, 114 "SEQUENCE_MATCH": 8, 115 "SEQUENCE_MISMATCH": 9, 116 } 117) 118 119func (x CigarUnit_Operation) Enum() *CigarUnit_Operation { 120 p := new(CigarUnit_Operation) 121 *p = x 122 return p 123} 124 125func (x CigarUnit_Operation) String() string { 126 return protoimpl.X.EnumStringOf(x.Descriptor(), protoreflect.EnumNumber(x)) 127} 128 129func (CigarUnit_Operation) Descriptor() protoreflect.EnumDescriptor { 130 return file_google_genomics_v1_cigar_proto_enumTypes[0].Descriptor() 131} 132 133func (CigarUnit_Operation) Type() protoreflect.EnumType { 134 return &file_google_genomics_v1_cigar_proto_enumTypes[0] 135} 136 137func (x CigarUnit_Operation) Number() protoreflect.EnumNumber { 138 return protoreflect.EnumNumber(x) 139} 140 141// Deprecated: Use CigarUnit_Operation.Descriptor instead. 142func (CigarUnit_Operation) EnumDescriptor() ([]byte, []int) { 143 return file_google_genomics_v1_cigar_proto_rawDescGZIP(), []int{0, 0} 144} 145 146// A single CIGAR operation. 147type CigarUnit struct { 148 state protoimpl.MessageState 149 sizeCache protoimpl.SizeCache 150 unknownFields protoimpl.UnknownFields 151 152 Operation CigarUnit_Operation `protobuf:"varint,1,opt,name=operation,proto3,enum=google.genomics.v1.CigarUnit_Operation" json:"operation,omitempty"` 153 // The number of genomic bases that the operation runs for. Required. 154 OperationLength int64 `protobuf:"varint,2,opt,name=operation_length,json=operationLength,proto3" json:"operation_length,omitempty"` 155 // `referenceSequence` is only used at mismatches 156 // (`SEQUENCE_MISMATCH`) and deletions (`DELETE`). 157 // Filling this field replaces SAM's MD tag. If the relevant information is 158 // not available, this field is unset. 159 ReferenceSequence string `protobuf:"bytes,3,opt,name=reference_sequence,json=referenceSequence,proto3" json:"reference_sequence,omitempty"` 160} 161 162func (x *CigarUnit) Reset() { 163 *x = CigarUnit{} 164 if protoimpl.UnsafeEnabled { 165 mi := &file_google_genomics_v1_cigar_proto_msgTypes[0] 166 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 167 ms.StoreMessageInfo(mi) 168 } 169} 170 171func (x *CigarUnit) String() string { 172 return protoimpl.X.MessageStringOf(x) 173} 174 175func (*CigarUnit) ProtoMessage() {} 176 177func (x *CigarUnit) ProtoReflect() protoreflect.Message { 178 mi := &file_google_genomics_v1_cigar_proto_msgTypes[0] 179 if protoimpl.UnsafeEnabled && x != nil { 180 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 181 if ms.LoadMessageInfo() == nil { 182 ms.StoreMessageInfo(mi) 183 } 184 return ms 185 } 186 return mi.MessageOf(x) 187} 188 189// Deprecated: Use CigarUnit.ProtoReflect.Descriptor instead. 190func (*CigarUnit) Descriptor() ([]byte, []int) { 191 return file_google_genomics_v1_cigar_proto_rawDescGZIP(), []int{0} 192} 193 194func (x *CigarUnit) GetOperation() CigarUnit_Operation { 195 if x != nil { 196 return x.Operation 197 } 198 return CigarUnit_OPERATION_UNSPECIFIED 199} 200 201func (x *CigarUnit) GetOperationLength() int64 { 202 if x != nil { 203 return x.OperationLength 204 } 205 return 0 206} 207 208func (x *CigarUnit) GetReferenceSequence() string { 209 if x != nil { 210 return x.ReferenceSequence 211 } 212 return "" 213} 214 215var File_google_genomics_v1_cigar_proto protoreflect.FileDescriptor 216 217var file_google_genomics_v1_cigar_proto_rawDesc = []byte{ 218 0x0a, 0x1e, 0x67, 0x6f, 0x6f, 0x67, 0x6c, 0x65, 0x2f, 0x67, 0x65, 0x6e, 0x6f, 0x6d, 0x69, 0x63, 219 0x73, 0x2f, 0x76, 0x31, 0x2f, 0x63, 0x69, 0x67, 0x61, 0x72, 0x2e, 0x70, 0x72, 0x6f, 0x74, 0x6f, 220 0x12, 0x12, 0x67, 0x6f, 0x6f, 0x67, 0x6c, 0x65, 0x2e, 0x67, 0x65, 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(*CigarUnit)(nil), // 1: google.genomics.v1.CigarUnit 272} 273var file_google_genomics_v1_cigar_proto_depIdxs = []int32{ 274 0, // 0: google.genomics.v1.CigarUnit.operation:type_name -> google.genomics.v1.CigarUnit.Operation 275 1, // [1:1] is the sub-list for method output_type 276 1, // [1:1] is the sub-list for method input_type 277 1, // [1:1] is the sub-list for extension type_name 278 1, // [1:1] is the sub-list for extension extendee 279 0, // [0:1] is the sub-list for field type_name 280} 281 282func init() { file_google_genomics_v1_cigar_proto_init() } 283func file_google_genomics_v1_cigar_proto_init() { 284 if File_google_genomics_v1_cigar_proto != nil { 285 return 286 } 287 if !protoimpl.UnsafeEnabled { 288 file_google_genomics_v1_cigar_proto_msgTypes[0].Exporter = func(v interface{}, i int) interface{} { 289 switch v := v.(*CigarUnit); i { 290 case 0: 291 return &v.state 292 case 1: 293 return &v.sizeCache 294 case 2: 295 return &v.unknownFields 296 default: 297 return nil 298 } 299 } 300 } 301 type x struct{} 302 out := protoimpl.TypeBuilder{ 303 File: protoimpl.DescBuilder{ 304 GoPackagePath: reflect.TypeOf(x{}).PkgPath(), 305 RawDescriptor: file_google_genomics_v1_cigar_proto_rawDesc, 306 NumEnums: 1, 307 NumMessages: 1, 308 NumExtensions: 0, 309 NumServices: 0, 310 }, 311 GoTypes: file_google_genomics_v1_cigar_proto_goTypes, 312 DependencyIndexes: file_google_genomics_v1_cigar_proto_depIdxs, 313 EnumInfos: file_google_genomics_v1_cigar_proto_enumTypes, 314 MessageInfos: file_google_genomics_v1_cigar_proto_msgTypes, 315 }.Build() 316 File_google_genomics_v1_cigar_proto = out.File 317 file_google_genomics_v1_cigar_proto_rawDesc = nil 318 file_google_genomics_v1_cigar_proto_goTypes = nil 319 file_google_genomics_v1_cigar_proto_depIdxs = nil 320} 321